Starting phenix.real_space_refine on Fri Mar 15 15:40:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c53_7342/03_2024/6c53_7342.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c53_7342/03_2024/6c53_7342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c53_7342/03_2024/6c53_7342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c53_7342/03_2024/6c53_7342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c53_7342/03_2024/6c53_7342.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c53_7342/03_2024/6c53_7342.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.010 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 7359 2.51 5 N 2112 2.21 5 O 2530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12023 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "B" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "C" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "D" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "E" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "F" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "G" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "H" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "I" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "J" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "K" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Time building chain proxies: 6.29, per 1000 atoms: 0.52 Number of scatterers: 12023 At special positions: 0 Unit cell: (82.95, 82.95, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 2530 8.00 N 2112 7.00 C 7359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 61 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 61 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 61 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 61 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 61 " distance=2.03 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 61 " distance=2.03 Simple disulfide: pdb=" SG CYS K 21 " - pdb=" SG CYS K 61 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 2.5 seconds 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 43 sheets defined 3.8% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL B 28 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL D 28 " --> pdb=" O ASP D 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL E 28 " --> pdb=" O ASP E 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.627A pdb=" N VAL F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 29 removed outlier: 3.627A pdb=" N VAL G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL H 28 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL I 28 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL J 28 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 29 removed outlier: 3.627A pdb=" N VAL K 28 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN A 6 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL B 156 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 74 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 37 removed outlier: 8.331A pdb=" N VAL B 37 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU A 15 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 22 through 23 removed outlier: 3.603A pdb=" N ALA A 22 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN A 59 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN A 129 " --> pdb=" O ASN A 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA5, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA6, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.577A pdb=" N LEU A 74 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL A 156 " --> pdb=" O ASN C 6 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN C 6 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN B 6 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL D 156 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 74 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 36 through 37 removed outlier: 8.330A pdb=" N VAL D 37 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU B 15 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA B 22 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN B 59 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN B 129 " --> pdb=" O ASN B 59 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA C 22 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN C 59 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN C 129 " --> pdb=" O ASN C 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB4, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AB5, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.576A pdb=" N LEU C 74 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL C 156 " --> pdb=" O ASN E 6 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN E 6 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN D 6 " --> pdb=" O VAL F 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL F 156 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU F 74 " --> pdb=" O THR F 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 36 through 37 removed outlier: 8.332A pdb=" N VAL F 37 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU D 15 " --> pdb=" O VAL F 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA D 22 " --> pdb=" O ASN D 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN D 59 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN D 129 " --> pdb=" O ASN D 59 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA E 22 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASN E 59 " --> pdb=" O ASN E 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN E 129 " --> pdb=" O ASN E 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 36 through 37 Processing sheet with id=AC3, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.575A pdb=" N LEU E 74 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL E 156 " --> pdb=" O ASN G 6 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN G 6 " --> pdb=" O VAL E 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN F 6 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL H 156 " --> pdb=" O ASN F 6 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU H 74 " --> pdb=" O THR H 153 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 36 through 37 removed outlier: 8.331A pdb=" N VAL H 37 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU F 15 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA F 22 " --> pdb=" O ASN F 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN F 59 " --> pdb=" O ASN F 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN F 129 " --> pdb=" O ASN F 59 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 52 through 54 Processing sheet with id=AC9, first strand: chain 'G' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA G 22 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN G 59 " --> pdb=" O ASN G 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN G 129 " --> pdb=" O ASN G 59 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 36 through 37 Processing sheet with id=AD2, first strand: chain 'G' and resid 52 through 54 Processing sheet with id=AD3, first strand: chain 'G' and resid 122 through 123 removed outlier: 3.576A pdb=" N LEU G 74 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL G 156 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN I 6 " --> pdb=" O VAL G 156 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN H 6 " --> pdb=" O VAL J 156 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL J 156 " --> pdb=" O ASN H 6 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU J 74 " --> pdb=" O THR J 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 36 through 37 removed outlier: 8.331A pdb=" N VAL J 37 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU H 15 " --> pdb=" O VAL J 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA H 22 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN H 59 " --> pdb=" O ASN H 129 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN H 129 " --> pdb=" O ASN H 59 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 52 through 54 Processing sheet with id=AD8, first strand: chain 'I' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA I 22 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN I 59 " --> pdb=" O ASN I 129 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASN I 129 " --> pdb=" O ASN I 59 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 36 through 37 Processing sheet with id=AE1, first strand: chain 'I' and resid 52 through 54 Processing sheet with id=AE2, first strand: chain 'I' and resid 122 through 123 removed outlier: 3.576A pdb=" N LEU I 74 " --> pdb=" O THR I 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL I 156 " --> pdb=" O ASN K 6 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASN K 6 " --> pdb=" O VAL I 156 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA J 22 " --> pdb=" O ASN J 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN J 59 " --> pdb=" O ASN J 129 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN J 129 " --> pdb=" O ASN J 59 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 52 through 54 Processing sheet with id=AE5, first strand: chain 'K' and resid 22 through 23 removed outlier: 3.603A pdb=" N ALA K 22 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN K 59 " --> pdb=" O ASN K 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN K 129 " --> pdb=" O ASN K 59 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 52 through 54 Processing sheet with id=AE7, first strand: chain 'K' and resid 122 through 123 removed outlier: 3.576A pdb=" N LEU K 74 " --> pdb=" O THR K 153 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4246 1.34 - 1.46: 2492 1.46 - 1.57: 5395 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 12155 Sorted by residual: bond pdb=" N THR E 3 " pdb=" CA THR E 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.55e+00 bond pdb=" N THR I 3 " pdb=" CA THR I 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.54e+00 bond pdb=" N THR J 3 " pdb=" CA THR J 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.46e+00 bond pdb=" N THR G 3 " pdb=" CA THR G 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.46e+00 bond pdb=" N THR B 3 " pdb=" CA THR B 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.44e+00 ... (remaining 12150 not shown) Histogram of bond angle deviations from ideal: 102.78 - 108.47: 608 108.47 - 114.17: 6729 114.17 - 119.86: 3125 119.86 - 125.55: 6082 125.55 - 131.24: 66 Bond angle restraints: 16610 Sorted by residual: angle pdb=" CA GLY J 75 " pdb=" C GLY J 75 " pdb=" N THR J 76 " ideal model delta sigma weight residual 115.34 117.69 -2.35 8.40e-01 1.42e+00 7.84e+00 angle pdb=" CA GLY A 75 " pdb=" C GLY A 75 " pdb=" N THR A 76 " ideal model delta sigma weight residual 115.34 117.66 -2.32 8.40e-01 1.42e+00 7.64e+00 angle pdb=" CA GLY E 75 " pdb=" C GLY E 75 " pdb=" N THR E 76 " ideal model delta sigma weight residual 115.34 117.66 -2.32 8.40e-01 1.42e+00 7.63e+00 angle pdb=" CA GLY B 75 " pdb=" C GLY B 75 " pdb=" N THR B 76 " ideal model delta sigma weight residual 115.34 117.65 -2.31 8.40e-01 1.42e+00 7.59e+00 angle pdb=" CA GLY C 75 " pdb=" C GLY C 75 " pdb=" N THR C 76 " ideal model delta sigma weight residual 115.34 117.65 -2.31 8.40e-01 1.42e+00 7.54e+00 ... (remaining 16605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 6721 14.78 - 29.55: 319 29.55 - 44.33: 22 44.33 - 59.10: 11 59.10 - 73.88: 11 Dihedral angle restraints: 7084 sinusoidal: 2277 harmonic: 4807 Sorted by residual: dihedral pdb=" CA SER H 50 " pdb=" C SER H 50 " pdb=" N ALA H 51 " pdb=" CA ALA H 51 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA SER A 50 " pdb=" C SER A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta harmonic sigma weight residual 180.00 -155.13 -24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA SER I 50 " pdb=" C SER I 50 " pdb=" N ALA I 51 " pdb=" CA ALA I 51 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1291 0.038 - 0.075: 553 0.075 - 0.113: 140 0.113 - 0.151: 84 0.151 - 0.189: 11 Chirality restraints: 2079 Sorted by residual: chirality pdb=" CA ILE E 56 " pdb=" N ILE E 56 " pdb=" C ILE E 56 " pdb=" CB ILE E 56 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA ILE K 56 " pdb=" N ILE K 56 " pdb=" C ILE K 56 " pdb=" CB ILE K 56 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA ILE B 56 " pdb=" N ILE B 56 " pdb=" C ILE B 56 " pdb=" CB ILE B 56 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.78e-01 ... (remaining 2076 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 144 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO K 145 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO K 145 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO K 145 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 144 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO I 145 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO I 145 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 145 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 144 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO C 145 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 145 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 145 " 0.029 5.00e-02 4.00e+02 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 806 2.70 - 3.25: 13039 3.25 - 3.80: 19384 3.80 - 4.35: 27058 4.35 - 4.90: 42511 Nonbonded interactions: 102798 Sorted by model distance: nonbonded pdb=" O VAL I 156 " pdb=" OG1 THR K 4 " model vdw 2.150 2.440 nonbonded pdb=" OG1 THR H 4 " pdb=" O VAL J 156 " model vdw 2.150 2.440 nonbonded pdb=" OG1 THR B 4 " pdb=" O VAL D 156 " model vdw 2.150 2.440 nonbonded pdb=" OG1 THR A 4 " pdb=" O VAL B 156 " model vdw 2.150 2.440 nonbonded pdb=" O VAL E 156 " pdb=" OG1 THR G 4 " model vdw 2.150 2.440 ... (remaining 102793 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.210 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.680 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12155 Z= 0.400 Angle : 0.923 6.365 16610 Z= 0.554 Chirality : 0.050 0.189 2079 Planarity : 0.004 0.051 2222 Dihedral : 9.181 73.877 3971 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.15), residues: 1694 helix: None (None), residues: 0 sheet: -2.78 (0.18), residues: 473 loop : -3.27 (0.14), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS D 11 PHE 0.008 0.002 PHE E 73 TYR 0.005 0.002 TYR H 137 ARG 0.002 0.001 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.9035 (t) cc_final: 0.8469 (t) REVERT: B 58 LEU cc_start: 0.8473 (mt) cc_final: 0.8136 (mm) REVERT: D 86 LEU cc_start: 0.8140 (tp) cc_final: 0.7935 (tt) REVERT: F 58 LEU cc_start: 0.8442 (mt) cc_final: 0.7520 (mm) REVERT: G 58 LEU cc_start: 0.8507 (mt) cc_final: 0.7670 (mm) REVERT: H 58 LEU cc_start: 0.8158 (mt) cc_final: 0.7362 (mm) REVERT: H 151 ASP cc_start: 0.7945 (t0) cc_final: 0.7708 (p0) REVERT: I 16 VAL cc_start: 0.9021 (t) cc_final: 0.8818 (t) REVERT: J 86 LEU cc_start: 0.8059 (tp) cc_final: 0.7802 (tt) REVERT: K 31 THR cc_start: 0.8601 (m) cc_final: 0.8396 (p) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2345 time to fit residues: 116.9584 Evaluate side-chains 171 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 50.0000 chunk 125 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 84 optimal weight: 50.0000 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 50 optimal weight: 30.0000 chunk 78 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 149 optimal weight: 50.0000 overall best weight: 10.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12155 Z= 0.251 Angle : 0.601 5.738 16610 Z= 0.336 Chirality : 0.042 0.139 2079 Planarity : 0.004 0.040 2222 Dihedral : 5.865 20.092 1760 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.18), residues: 1694 helix: -3.26 (0.45), residues: 66 sheet: -1.66 (0.21), residues: 473 loop : -2.42 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 11 PHE 0.017 0.002 PHE B 118 TYR 0.015 0.003 TYR E 137 ARG 0.009 0.002 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8140 (m-10) cc_final: 0.7857 (m-10) REVERT: B 15 GLU cc_start: 0.8060 (tp30) cc_final: 0.7798 (tp30) REVERT: B 88 LEU cc_start: 0.8802 (mt) cc_final: 0.8587 (mt) REVERT: B 151 ASP cc_start: 0.8313 (t70) cc_final: 0.8084 (t70) REVERT: F 151 ASP cc_start: 0.8333 (t70) cc_final: 0.8063 (t70) REVERT: H 12 PHE cc_start: 0.8451 (m-80) cc_final: 0.8199 (m-80) REVERT: I 42 LEU cc_start: 0.8937 (mm) cc_final: 0.8693 (mt) REVERT: J 138 PHE cc_start: 0.8336 (t80) cc_final: 0.8131 (t80) REVERT: K 34 LEU cc_start: 0.8369 (tt) cc_final: 0.8135 (tt) REVERT: K 42 LEU cc_start: 0.8997 (mm) cc_final: 0.8727 (mt) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1923 time to fit residues: 76.2848 Evaluate side-chains 148 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 50.0000 chunk 46 optimal weight: 20.0000 chunk 124 optimal weight: 50.0000 chunk 102 optimal weight: 50.0000 chunk 41 optimal weight: 0.0070 chunk 150 optimal weight: 50.0000 chunk 162 optimal weight: 50.0000 chunk 133 optimal weight: 8.9990 chunk 148 optimal weight: 40.0000 chunk 51 optimal weight: 50.0000 chunk 120 optimal weight: 30.0000 overall best weight: 19.8012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 HIS K 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 12155 Z= 0.393 Angle : 0.683 6.925 16610 Z= 0.377 Chirality : 0.043 0.141 2079 Planarity : 0.004 0.039 2222 Dihedral : 6.203 22.704 1760 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.16 % Allowed : 3.77 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.17), residues: 1694 helix: -3.07 (0.50), residues: 66 sheet: -1.40 (0.21), residues: 495 loop : -2.37 (0.15), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 11 PHE 0.018 0.003 PHE H 118 TYR 0.014 0.003 TYR I 137 ARG 0.006 0.002 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 203 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8364 (m-10) cc_final: 0.8152 (m-80) REVERT: A 60 ASP cc_start: 0.6975 (m-30) cc_final: 0.6540 (m-30) REVERT: A 88 LEU cc_start: 0.9006 (mt) cc_final: 0.8722 (mt) REVERT: A 103 ILE cc_start: 0.9135 (tp) cc_final: 0.8855 (mm) REVERT: B 60 ASP cc_start: 0.7234 (m-30) cc_final: 0.6786 (m-30) REVERT: B 88 LEU cc_start: 0.8970 (mt) cc_final: 0.8748 (mt) REVERT: C 60 ASP cc_start: 0.7294 (m-30) cc_final: 0.7031 (m-30) REVERT: C 62 ASP cc_start: 0.8351 (t0) cc_final: 0.8141 (t0) REVERT: D 12 PHE cc_start: 0.8306 (m-80) cc_final: 0.7424 (m-10) REVERT: D 60 ASP cc_start: 0.6923 (m-30) cc_final: 0.6593 (m-30) REVERT: E 60 ASP cc_start: 0.7199 (m-30) cc_final: 0.6800 (m-30) REVERT: E 103 ILE cc_start: 0.9060 (tp) cc_final: 0.8788 (mm) REVERT: F 60 ASP cc_start: 0.7543 (m-30) cc_final: 0.6935 (m-30) REVERT: F 103 ILE cc_start: 0.9046 (tp) cc_final: 0.8832 (mm) REVERT: G 33 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8378 (tp40) REVERT: G 62 ASP cc_start: 0.7982 (t0) cc_final: 0.7777 (t0) REVERT: G 103 ILE cc_start: 0.8959 (tp) cc_final: 0.8701 (mm) REVERT: H 60 ASP cc_start: 0.7482 (m-30) cc_final: 0.7106 (m-30) REVERT: I 12 PHE cc_start: 0.8226 (m-80) cc_final: 0.7683 (m-80) REVERT: I 42 LEU cc_start: 0.9040 (mm) cc_final: 0.8760 (mt) REVERT: J 84 ASN cc_start: 0.8680 (m-40) cc_final: 0.8303 (p0) outliers start: 2 outliers final: 1 residues processed: 205 average time/residue: 0.2071 time to fit residues: 63.6356 Evaluate side-chains 135 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 50.0000 chunk 112 optimal weight: 50.0000 chunk 77 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 40.0000 chunk 100 optimal weight: 50.0000 chunk 150 optimal weight: 50.0000 chunk 159 optimal weight: 50.0000 chunk 78 optimal weight: 5.9990 chunk 142 optimal weight: 50.0000 chunk 42 optimal weight: 20.0000 overall best weight: 15.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN J 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 12155 Z= 0.315 Angle : 0.609 5.901 16610 Z= 0.337 Chirality : 0.041 0.132 2079 Planarity : 0.004 0.037 2222 Dihedral : 5.725 21.094 1760 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 26.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.18), residues: 1694 helix: -2.88 (0.53), residues: 66 sheet: -0.91 (0.23), residues: 451 loop : -2.05 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 11 PHE 0.016 0.003 PHE H 118 TYR 0.010 0.002 TYR K 158 ARG 0.005 0.001 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.6913 (m-30) cc_final: 0.6602 (m-30) REVERT: A 88 LEU cc_start: 0.8932 (mt) cc_final: 0.8674 (mt) REVERT: B 60 ASP cc_start: 0.7055 (m-30) cc_final: 0.6686 (m-30) REVERT: B 88 LEU cc_start: 0.8872 (mt) cc_final: 0.8565 (mt) REVERT: B 136 ARG cc_start: 0.8138 (ptt180) cc_final: 0.7743 (ptt180) REVERT: C 60 ASP cc_start: 0.7303 (m-30) cc_final: 0.6903 (m-30) REVERT: D 12 PHE cc_start: 0.8279 (m-80) cc_final: 0.7946 (m-10) REVERT: E 60 ASP cc_start: 0.7144 (m-30) cc_final: 0.6806 (m-30) REVERT: E 103 ILE cc_start: 0.9074 (tp) cc_final: 0.8842 (mm) REVERT: F 60 ASP cc_start: 0.7074 (m-30) cc_final: 0.6682 (m-30) REVERT: F 151 ASP cc_start: 0.8489 (t70) cc_final: 0.8066 (t0) REVERT: F 154 PHE cc_start: 0.7957 (t80) cc_final: 0.7734 (t80) REVERT: H 60 ASP cc_start: 0.6816 (m-30) cc_final: 0.6534 (m-30) REVERT: I 12 PHE cc_start: 0.8259 (m-80) cc_final: 0.7896 (m-80) REVERT: I 88 LEU cc_start: 0.8798 (mt) cc_final: 0.8569 (mt) REVERT: I 154 PHE cc_start: 0.7763 (t80) cc_final: 0.7552 (t80) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2107 time to fit residues: 58.6899 Evaluate side-chains 127 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 50.0000 chunk 90 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 chunk 118 optimal weight: 50.0000 chunk 65 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 110 optimal weight: 40.0000 chunk 0 optimal weight: 60.0000 chunk 81 optimal weight: 30.0000 chunk 143 optimal weight: 30.0000 chunk 40 optimal weight: 0.1980 overall best weight: 10.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN K 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12155 Z= 0.230 Angle : 0.555 6.092 16610 Z= 0.302 Chirality : 0.040 0.128 2079 Planarity : 0.003 0.036 2222 Dihedral : 5.101 18.161 1760 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.18), residues: 1694 helix: -2.74 (0.55), residues: 66 sheet: -0.78 (0.22), residues: 473 loop : -1.93 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 11 PHE 0.013 0.002 PHE J 154 TYR 0.010 0.002 TYR E 137 ARG 0.004 0.001 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.6828 (m-30) cc_final: 0.6535 (m-30) REVERT: A 88 LEU cc_start: 0.8863 (mt) cc_final: 0.8350 (mt) REVERT: B 60 ASP cc_start: 0.6993 (m-30) cc_final: 0.6613 (m-30) REVERT: B 88 LEU cc_start: 0.8903 (mt) cc_final: 0.8636 (mt) REVERT: B 136 ARG cc_start: 0.8106 (ptt180) cc_final: 0.7822 (ptt180) REVERT: C 12 PHE cc_start: 0.8457 (m-80) cc_final: 0.8178 (m-10) REVERT: C 151 ASP cc_start: 0.8226 (t0) cc_final: 0.7941 (t0) REVERT: D 12 PHE cc_start: 0.8352 (m-80) cc_final: 0.7920 (m-10) REVERT: D 60 ASP cc_start: 0.7284 (m-30) cc_final: 0.6882 (m-30) REVERT: D 151 ASP cc_start: 0.8378 (t70) cc_final: 0.8094 (t0) REVERT: E 60 ASP cc_start: 0.7004 (m-30) cc_final: 0.6708 (m-30) REVERT: E 103 ILE cc_start: 0.9086 (tp) cc_final: 0.8857 (mm) REVERT: F 60 ASP cc_start: 0.6930 (m-30) cc_final: 0.6532 (m-30) REVERT: G 79 ASP cc_start: 0.7194 (m-30) cc_final: 0.6951 (p0) REVERT: H 60 ASP cc_start: 0.6862 (m-30) cc_final: 0.6619 (m-30) REVERT: I 12 PHE cc_start: 0.8194 (m-80) cc_final: 0.7742 (m-80) REVERT: I 33 GLN cc_start: 0.9006 (tp40) cc_final: 0.8783 (tp40) REVERT: I 42 LEU cc_start: 0.9048 (mm) cc_final: 0.8823 (mt) REVERT: K 84 ASN cc_start: 0.8701 (m-40) cc_final: 0.8290 (p0) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2059 time to fit residues: 62.1103 Evaluate side-chains 134 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 30.0000 chunk 143 optimal weight: 30.0000 chunk 31 optimal weight: 50.0000 chunk 93 optimal weight: 40.0000 chunk 39 optimal weight: 50.0000 chunk 159 optimal weight: 50.0000 chunk 132 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 83 optimal weight: 40.0000 overall best weight: 15.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 12155 Z= 0.306 Angle : 0.601 6.417 16610 Z= 0.329 Chirality : 0.040 0.133 2079 Planarity : 0.004 0.034 2222 Dihedral : 5.409 20.139 1760 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.18), residues: 1694 helix: -2.50 (0.60), residues: 66 sheet: -0.79 (0.22), residues: 473 loop : -1.93 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 11 PHE 0.023 0.002 PHE H 54 TYR 0.012 0.002 TYR A 158 ARG 0.007 0.001 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.9097 (tp) cc_final: 0.8877 (mm) REVERT: B 60 ASP cc_start: 0.7201 (m-30) cc_final: 0.6790 (m-30) REVERT: B 88 LEU cc_start: 0.8932 (mt) cc_final: 0.8634 (mt) REVERT: C 60 ASP cc_start: 0.7416 (m-30) cc_final: 0.7198 (m-30) REVERT: D 12 PHE cc_start: 0.8385 (m-80) cc_final: 0.8156 (m-10) REVERT: D 60 ASP cc_start: 0.7388 (m-30) cc_final: 0.7002 (m-30) REVERT: D 154 PHE cc_start: 0.7560 (t80) cc_final: 0.7156 (t80) REVERT: E 60 ASP cc_start: 0.7189 (m-30) cc_final: 0.6869 (m-30) REVERT: E 103 ILE cc_start: 0.9079 (tp) cc_final: 0.8856 (mm) REVERT: F 13 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8096 (mmmt) REVERT: F 60 ASP cc_start: 0.7105 (m-30) cc_final: 0.6718 (m-30) REVERT: G 88 LEU cc_start: 0.8914 (mt) cc_final: 0.8634 (mt) REVERT: H 60 ASP cc_start: 0.7022 (m-30) cc_final: 0.6758 (m-30) REVERT: I 12 PHE cc_start: 0.8315 (m-80) cc_final: 0.8109 (m-80) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2057 time to fit residues: 53.4975 Evaluate side-chains 132 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 10.0000 chunk 17 optimal weight: 40.0000 chunk 90 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 89 optimal weight: 40.0000 chunk 159 optimal weight: 50.0000 chunk 99 optimal weight: 50.0000 chunk 96 optimal weight: 50.0000 chunk 73 optimal weight: 20.0000 chunk 98 optimal weight: 40.0000 overall best weight: 15.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 12155 Z= 0.309 Angle : 0.604 6.409 16610 Z= 0.330 Chirality : 0.040 0.132 2079 Planarity : 0.003 0.034 2222 Dihedral : 5.495 20.661 1760 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.18), residues: 1694 helix: -2.45 (0.59), residues: 66 sheet: -0.79 (0.22), residues: 451 loop : -1.90 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 11 PHE 0.014 0.002 PHE H 118 TYR 0.013 0.002 TYR C 158 ARG 0.006 0.001 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8804 (mt) cc_final: 0.8523 (mt) REVERT: A 103 ILE cc_start: 0.9088 (tp) cc_final: 0.8863 (mm) REVERT: B 60 ASP cc_start: 0.7361 (m-30) cc_final: 0.6953 (m-30) REVERT: B 88 LEU cc_start: 0.8939 (mt) cc_final: 0.8630 (mt) REVERT: C 60 ASP cc_start: 0.7470 (m-30) cc_final: 0.7042 (m-30) REVERT: D 60 ASP cc_start: 0.7431 (m-30) cc_final: 0.6982 (m-30) REVERT: E 60 ASP cc_start: 0.7220 (m-30) cc_final: 0.6935 (m-30) REVERT: E 103 ILE cc_start: 0.9041 (tp) cc_final: 0.8832 (mm) REVERT: F 60 ASP cc_start: 0.7292 (m-30) cc_final: 0.6903 (m-30) REVERT: G 60 ASP cc_start: 0.7258 (m-30) cc_final: 0.6819 (m-30) REVERT: H 12 PHE cc_start: 0.8235 (m-80) cc_final: 0.7958 (m-80) REVERT: H 60 ASP cc_start: 0.7019 (m-30) cc_final: 0.6751 (m-30) REVERT: I 12 PHE cc_start: 0.8375 (m-80) cc_final: 0.8174 (m-80) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2132 time to fit residues: 54.7777 Evaluate side-chains 129 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 40.0000 chunk 94 optimal weight: 50.0000 chunk 47 optimal weight: 30.0000 chunk 31 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 chunk 101 optimal weight: 40.0000 chunk 108 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 14 optimal weight: 30.0000 chunk 125 optimal weight: 10.0000 chunk 144 optimal weight: 50.0000 overall best weight: 15.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.6616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 12155 Z= 0.314 Angle : 0.620 6.443 16610 Z= 0.338 Chirality : 0.041 0.131 2079 Planarity : 0.004 0.033 2222 Dihedral : 5.625 21.697 1760 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 26.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.18), residues: 1694 helix: -2.26 (0.62), residues: 66 sheet: -0.94 (0.21), residues: 473 loop : -1.92 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 11 PHE 0.018 0.002 PHE E 118 TYR 0.014 0.002 TYR E 158 ARG 0.006 0.001 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.9063 (tp) cc_final: 0.8833 (mm) REVERT: B 60 ASP cc_start: 0.7517 (m-30) cc_final: 0.7106 (m-30) REVERT: B 88 LEU cc_start: 0.8951 (mt) cc_final: 0.8641 (mt) REVERT: C 60 ASP cc_start: 0.7598 (m-30) cc_final: 0.7112 (m-30) REVERT: D 60 ASP cc_start: 0.7608 (m-30) cc_final: 0.7211 (m-30) REVERT: E 60 ASP cc_start: 0.7267 (m-30) cc_final: 0.6993 (m-30) REVERT: E 103 ILE cc_start: 0.9052 (tp) cc_final: 0.8850 (mm) REVERT: F 60 ASP cc_start: 0.7402 (m-30) cc_final: 0.6977 (m-30) REVERT: G 60 ASP cc_start: 0.7390 (m-30) cc_final: 0.6969 (m-30) REVERT: G 88 LEU cc_start: 0.8807 (mt) cc_final: 0.8606 (mt) REVERT: H 12 PHE cc_start: 0.8243 (m-80) cc_final: 0.8024 (m-80) REVERT: H 60 ASP cc_start: 0.7127 (m-30) cc_final: 0.6810 (m-30) REVERT: I 12 PHE cc_start: 0.8382 (m-80) cc_final: 0.8130 (m-80) REVERT: K 79 ASP cc_start: 0.7441 (m-30) cc_final: 0.7054 (p0) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2088 time to fit residues: 52.0863 Evaluate side-chains 128 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 30.0000 chunk 139 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 89 optimal weight: 50.0000 chunk 64 optimal weight: 9.9990 chunk 116 optimal weight: 40.0000 chunk 45 optimal weight: 50.0000 chunk 133 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 97 optimal weight: 50.0000 overall best weight: 11.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12155 Z= 0.248 Angle : 0.589 6.748 16610 Z= 0.317 Chirality : 0.041 0.131 2079 Planarity : 0.003 0.033 2222 Dihedral : 5.325 19.355 1760 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 24.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.19), residues: 1694 helix: -2.10 (0.63), residues: 66 sheet: -0.88 (0.22), residues: 473 loop : -1.84 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 11 PHE 0.017 0.002 PHE E 118 TYR 0.010 0.002 TYR B 158 ARG 0.004 0.001 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ASP cc_start: 0.7510 (m-30) cc_final: 0.7098 (m-30) REVERT: B 88 LEU cc_start: 0.8938 (mt) cc_final: 0.8668 (mt) REVERT: C 60 ASP cc_start: 0.7473 (m-30) cc_final: 0.6994 (m-30) REVERT: C 84 ASN cc_start: 0.8721 (m-40) cc_final: 0.8262 (p0) REVERT: E 60 ASP cc_start: 0.7187 (m-30) cc_final: 0.6971 (m-30) REVERT: F 60 ASP cc_start: 0.7419 (m-30) cc_final: 0.7018 (m-30) REVERT: G 60 ASP cc_start: 0.7316 (m-30) cc_final: 0.6827 (m-30) REVERT: G 79 ASP cc_start: 0.7156 (m-30) cc_final: 0.6941 (p0) REVERT: G 88 LEU cc_start: 0.8830 (mt) cc_final: 0.8592 (mt) REVERT: H 12 PHE cc_start: 0.8232 (m-80) cc_final: 0.7971 (m-80) REVERT: H 60 ASP cc_start: 0.7265 (m-30) cc_final: 0.6896 (m-30) REVERT: I 42 LEU cc_start: 0.8956 (mm) cc_final: 0.8552 (mt) REVERT: I 44 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7613 (pm20) REVERT: K 79 ASP cc_start: 0.7347 (m-30) cc_final: 0.7124 (p0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2097 time to fit residues: 56.0029 Evaluate side-chains 134 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 20.0000 chunk 95 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 108 optimal weight: 40.0000 chunk 164 optimal weight: 10.0000 chunk 151 optimal weight: 30.0000 chunk 130 optimal weight: 50.0000 chunk 13 optimal weight: 30.0000 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 overall best weight: 14.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12155 Z= 0.293 Angle : 0.614 7.186 16610 Z= 0.332 Chirality : 0.041 0.131 2079 Planarity : 0.003 0.035 2222 Dihedral : 5.532 21.131 1760 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.19), residues: 1694 helix: -2.11 (0.64), residues: 66 sheet: -0.87 (0.22), residues: 473 loop : -1.84 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 82 PHE 0.016 0.002 PHE B 118 TYR 0.011 0.002 TYR E 137 ARG 0.005 0.001 ARG G 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ASP cc_start: 0.7497 (m-30) cc_final: 0.7047 (m-30) REVERT: B 88 LEU cc_start: 0.8945 (mt) cc_final: 0.8681 (mt) REVERT: C 60 ASP cc_start: 0.7507 (m-30) cc_final: 0.7013 (m-30) REVERT: D 60 ASP cc_start: 0.7650 (m-30) cc_final: 0.7286 (m-30) REVERT: E 60 ASP cc_start: 0.7255 (m-30) cc_final: 0.7043 (m-30) REVERT: F 60 ASP cc_start: 0.7433 (m-30) cc_final: 0.7087 (m-30) REVERT: G 60 ASP cc_start: 0.7374 (m-30) cc_final: 0.6835 (m-30) REVERT: G 88 LEU cc_start: 0.8821 (mt) cc_final: 0.8592 (mt) REVERT: H 60 ASP cc_start: 0.7356 (m-30) cc_final: 0.6964 (m-30) REVERT: I 12 PHE cc_start: 0.8405 (m-80) cc_final: 0.8003 (m-10) REVERT: K 79 ASP cc_start: 0.7411 (m-30) cc_final: 0.7121 (p0) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2082 time to fit residues: 50.3326 Evaluate side-chains 127 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 30.0000 chunk 40 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 19 optimal weight: 40.0000 chunk 36 optimal weight: 40.0000 chunk 131 optimal weight: 9.9990 chunk 54 optimal weight: 50.0000 chunk 134 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 115 optimal weight: 50.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.065676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059149 restraints weight = 59204.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.060854 restraints weight = 35394.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.062008 restraints weight = 23002.348| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.6901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12155 Z= 0.196 Angle : 0.570 7.414 16610 Z= 0.304 Chirality : 0.041 0.177 2079 Planarity : 0.003 0.033 2222 Dihedral : 5.037 17.170 1760 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 23.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.19), residues: 1694 helix: -1.83 (0.65), residues: 66 sheet: -0.71 (0.23), residues: 451 loop : -1.73 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 11 PHE 0.015 0.002 PHE B 118 TYR 0.011 0.002 TYR E 137 ARG 0.008 0.001 ARG B 136 =============================================================================== Job complete usr+sys time: 1991.86 seconds wall clock time: 37 minutes 40.26 seconds (2260.26 seconds total)